AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1029430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1029430 MtrunA17_Chr7g0249821 95.062 81 3 1 1 80 1 81 1.58e-54 164
Msa1029430 MtrunA17_Chr7g0249831 68.293 82 24 2 1 80 1 82 5.34e-33 110
Msa1029430 MtrunA17_Chr5g0396151 67.073 82 25 2 1 80 1 82 1.00e-32 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1029430 AT4G10040.1 68.293 82 24 2 1 80 1 82 1.08e-32 109
Msa1029430 AT1G22840.2 65.116 86 28 2 1 84 1 86 1.42e-31 106
Msa1029430 AT1G22840.1 65.854 82 26 2 1 80 1 82 8.16e-31 105

Find 28 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCACCGGCAGCACGGTTTC+TGG 0.212914 7_1:-62870448 None:intergenic
ATGTGTTGTTTGTACCTTCT+TGG 0.279033 7_1:-62870812 None:intergenic
CCCAATCTGAATGGTTTGTT+TGG 0.305862 7_1:+62870688 Msa1029430:CDS
TGTGTTGTTTGTACCTTCTT+GGG 0.313440 7_1:-62870811 None:intergenic
ACAAGAACATGTCTATGAAT+TGG 0.322531 7_1:+62870755 Msa1029430:CDS
GCAAAACAATATGAATATTC+AGG 0.322686 7_1:-62870730 None:intergenic
GGTTTGTTTGGAAGTCAATC+TGG 0.344506 7_1:+62870700 Msa1029430:CDS
GTGCTGCCGGTGAGAAGTTC+AGG 0.352217 7_1:+62870457 Msa1029430:CDS
TCACCGGCAGCACGGTTTCT+GGG 0.386514 7_1:-62870447 None:intergenic
CAAGAACATGTCTATGAATT+GGG 0.403729 7_1:+62870756 Msa1029430:CDS
TCCAAACAAACCATTCAGAT+TGG 0.443064 7_1:-62870689 None:intergenic
GTACCTTCTTGGGGTTAAGC+AGG 0.468483 7_1:-62870801 None:intergenic
ACCTTAGGACCCAATCTGAA+TGG 0.493293 7_1:+62870679 Msa1029430:intron
CCAAACAAACCATTCAGATT+GGG 0.496498 7_1:-62870688 None:intergenic
TTTGTGAACGGCTCCTATGT+TGG 0.508283 7_1:-62870502 None:intergenic
TATTAAACCTTGTTTGTGAA+CGG 0.508923 7_1:-62870514 None:intergenic
CTTCCCAGAAACCGTGCTGC+CGG 0.509379 7_1:+62870444 Msa1029430:CDS
GTTTGTTTGGAAGTCAATCT+GGG 0.526603 7_1:+62870701 Msa1029430:CDS
GCTCAATGCCACACCAACAT+AGG 0.557024 7_1:+62870489 Msa1029430:CDS
GAATTGGGAGGAAAAGATCA+TGG 0.562314 7_1:+62870771 Msa1029430:CDS
GCACGGTTTCTGGGAAGTGT+CGG 0.562820 7_1:-62870438 None:intergenic
GTGTTGTTTGTACCTTCTTG+GGG 0.564448 7_1:-62870810 None:intergenic
ATAGGAGCCGTTCACAAACA+AGG 0.604312 7_1:+62870507 Msa1029430:CDS
TGAACTTCTCACCGGCAGCA+CGG 0.620657 7_1:-62870455 None:intergenic
ATCACTCCTGAACTTCTCAC+CGG 0.651892 7_1:-62870463 None:intergenic
GAACATGTCTATGAATTGGG+AGG 0.658810 7_1:+62870759 Msa1029430:CDS
TTACCTGCTTAACCCCAAGA+AGG 0.666741 7_1:+62870798 Msa1029430:CDS
GAACGGCTCCTATGTTGGTG+TGG 0.672356 7_1:-62870497 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAAACCTTGTTTGTGAA+CGG - chr7_1:62870517-62870536 None:intergenic 25.0%
! GTAAATCTGAGAGTTTATTT+AGG - chr7_1:62870556-62870575 None:intergenic 25.0%
!!! TTTTATTTGTTGTCAACCTT+AGG + chr7_1:62870664-62870683 Msa1029430:intron 25.0%
! GCAAAACAATATGAATATTC+AGG - chr7_1:62870733-62870752 None:intergenic 25.0%
ATGATGACATATATTCAAGC+AGG - chr7_1:62870614-62870633 None:intergenic 30.0%
ACAAGAACATGTCTATGAAT+TGG + chr7_1:62870755-62870774 Msa1029430:CDS 30.0%
CAAGAACATGTCTATGAATT+GGG + chr7_1:62870756-62870775 Msa1029430:CDS 30.0%
CCAAACAAACCATTCAGATT+GGG - chr7_1:62870691-62870710 None:intergenic 35.0%
TCCAAACAAACCATTCAGAT+TGG - chr7_1:62870692-62870711 None:intergenic 35.0%
GTTTGTTTGGAAGTCAATCT+GGG + chr7_1:62870701-62870720 Msa1029430:CDS 35.0%
!! TGTGTTGTTTGTACCTTCTT+GGG - chr7_1:62870814-62870833 None:intergenic 35.0%
!! ATGTGTTGTTTGTACCTTCT+TGG - chr7_1:62870815-62870834 None:intergenic 35.0%
!! CCCAATCTGAATGGTTTGTT+TGG + chr7_1:62870688-62870707 Msa1029430:CDS 40.0%
! GGTTTGTTTGGAAGTCAATC+TGG + chr7_1:62870700-62870719 Msa1029430:CDS 40.0%
GAACATGTCTATGAATTGGG+AGG + chr7_1:62870759-62870778 Msa1029430:CDS 40.0%
GAATTGGGAGGAAAAGATCA+TGG + chr7_1:62870771-62870790 Msa1029430:CDS 40.0%
!! GTGTTGTTTGTACCTTCTTG+GGG - chr7_1:62870813-62870832 None:intergenic 40.0%
ATCACTCCTGAACTTCTCAC+CGG - chr7_1:62870466-62870485 None:intergenic 45.0%
TTTGTGAACGGCTCCTATGT+TGG - chr7_1:62870505-62870524 None:intergenic 45.0%
ATAGGAGCCGTTCACAAACA+AGG + chr7_1:62870507-62870526 Msa1029430:CDS 45.0%
ACCTTAGGACCCAATCTGAA+TGG + chr7_1:62870679-62870698 Msa1029430:intron 45.0%
ACCATTCAGATTGGGTCCTA+AGG - chr7_1:62870683-62870702 None:intergenic 45.0%
TTACCTGCTTAACCCCAAGA+AGG + chr7_1:62870798-62870817 Msa1029430:CDS 45.0%
GCTCAATGCCACACCAACAT+AGG + chr7_1:62870489-62870508 Msa1029430:CDS 50.0%
GTACCTTCTTGGGGTTAAGC+AGG - chr7_1:62870804-62870823 None:intergenic 50.0%
! GCACGGTTTCTGGGAAGTGT+CGG - chr7_1:62870441-62870460 None:intergenic 55.0%
TGAACTTCTCACCGGCAGCA+CGG - chr7_1:62870458-62870477 None:intergenic 55.0%
GAACGGCTCCTATGTTGGTG+TGG - chr7_1:62870500-62870519 None:intergenic 55.0%
CTTCCCAGAAACCGTGCTGC+CGG + chr7_1:62870444-62870463 Msa1029430:CDS 60.0%
TCACCGGCAGCACGGTTTCT+GGG - chr7_1:62870450-62870469 None:intergenic 60.0%
GTGCTGCCGGTGAGAAGTTC+AGG + chr7_1:62870457-62870476 Msa1029430:CDS 60.0%
CTCACCGGCAGCACGGTTTC+TGG - chr7_1:62870451-62870470 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 62870423 62870837 62870423 ID=Msa1029430;Name=Msa1029430
chr7_1 mRNA 62870423 62870837 62870423 ID=Msa1029430-mRNA-1;Parent=Msa1029430;Name=Msa1029430-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|0|0|1|1|1|2|0|85
chr7_1 exon 62870423 62870528 62870423 ID=Msa1029430-mRNA-1:exon:13530;Parent=Msa1029430-mRNA-1
chr7_1 exon 62870686 62870837 62870686 ID=Msa1029430-mRNA-1:exon:13531;Parent=Msa1029430-mRNA-1
chr7_1 CDS 62870423 62870528 62870423 ID=Msa1029430-mRNA-1:cds;Parent=Msa1029430-mRNA-1
chr7_1 CDS 62870686 62870837 62870686 ID=Msa1029430-mRNA-1:cds;Parent=Msa1029430-mRNA-1
Gene Sequence

>Msa1029430

ATGGAGTTGTTCGAACCGACACTTCCCAGAAACCGTGCTGCCGGTGAGAAGTTCAGGAGTGATTGCGCTCAATGCCACACCAACATAGGAGCCGTTCACAAACAAGGACCCAATCTGAATGGTTTGTTTGGAAGTCAATCTGGGACAACTCCTGAATATTCATATTGTTTTGCTAACAAGAACATGTCTATGAATTGGGAGGAAAAGATCATGGATGATTACCTGCTTAACCCCAAGAAGGTACAAACAACACATTGA

Protein sequence

>Msa1029430

MELFEPTLPRNRAAGEKFRSDCAQCHTNIGAVHKQGPNLNGLFGSQSGTTPEYSYCFANKNMSMNWEEKIMDDYLLNPKKVQTTH*